Contacts of the helix formed by residues 9 - 26 (chain L) in PDB entry 3J9X
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with SER 9 (chain L).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53K THR* 4.2 5.8 - - - -
8L ARG* 1.3 76.6 - - - +
10L TYR* 1.3 64.9 + - - +
11L SER* 2.7 28.2 + - - -
12L GLN* 2.8 23.5 + - - +
13L ARG* 3.0 20.8 + - - +
47p THR* 5.8 7.1 - - - -
50p PRO* 6.4 2.5 - - - -
51p LYS* 6.4 2.2 - - - -
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Residues in contact with TYR 10 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45K PHE* 5.1 0.4 - + - -
46K GLN* 5.2 13.1 + - + +
49K VAL* 4.6 6.3 - - + -
50K PRO* 3.7 35.0 - - + -
53K THR* 3.1 39.7 - - + +
9L SER* 1.3 75.4 - - - +
11L SER* 1.3 77.3 + - - +
13L ARG* 3.4 6.8 - - - +
14L TYR* 2.8 49.5 + + + -
10o TYR* 2.8 47.5 + + - -
11o SER* 5.0 3.8 + - - -
14o TYR* 5.5 1.7 - - - -
50p PRO* 4.1 17.3 - - + -
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Residues in contact with SER 11 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9L SER* 2.7 21.7 + - - -
10L TYR* 1.3 101.3 - - - +
12L GLN* 1.3 59.3 + - - +
14L TYR* 3.9 3.8 - - - +
15L ALA* 2.9 29.9 + - - +
43p GLN* 5.2 6.1 + - - -
46p GLN* 4.3 36.7 + - - +
47p THR* 5.0 4.0 + - - -
50p PRO* 5.7 0.7 - - - -
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Residues in contact with GLN 12 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
738 A 4.1 3.3 + - - -
7L SER 4.7 2.1 + - - +
8L ARG* 3.6 27.8 - - - +
9L SER* 2.8 38.8 + - - +
10L TYR 3.1 0.4 - - - -
11L SER* 1.3 84.4 + - - +
13L ARG* 1.3 63.4 + - - +
15L ALA* 3.7 5.8 - - - +
16L LYS* 3.1 25.6 + - - +
40M VAL* 5.0 2.6 - - - +
43M GLN* 5.3 7.4 - - + +
44M ASN* 2.9 32.8 + - - +
47M THR* 4.9 15.0 + - - +
48M ASN* 5.5 2.8 - - - +
43p GLN* 6.2 2.0 - - - +
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Residues in contact with ARG 13 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2777 A 3.9 15.2 + - - -
2787 T 4.8 5.3 + - - -
728 T 3.8 31.0 + - + +
738 A 3.6 57.5 + - - +
45K PHE* 4.5 7.7 - - + -
49K VAL* 3.8 20.7 + - + +
52K PHE* 4.5 4.0 - - - +
53K THR* 2.7 48.0 + - - +
56K ASN* 4.0 11.7 - - - +
8L ARG* 4.3 8.7 - - + -
9L SER 3.0 21.0 + - - +
10L TYR* 3.4 6.7 - - - +
12L GLN* 1.3 77.1 - - - +
14L TYR* 1.3 56.9 + - - +
16L LYS 3.7 0.2 + - - -
17L TRP* 3.0 29.4 + - - +
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Residues in contact with TYR 14 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42K GLN* 3.9 10.1 + - - +
45K PHE* 3.5 33.8 - + + -
46K GLN* 3.4 41.6 + - + -
10L TYR* 2.8 35.9 + + + +
11L SER* 3.9 4.5 - - - +
13L ARG* 1.3 75.8 - - - +
15L ALA* 1.3 71.0 + - + +
17L TRP* 3.0 14.2 + + - -
18L GLN* 2.7 58.7 + - + +
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Residues in contact with ALA 15 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11L SER 2.9 18.8 + - - +
12L GLN* 3.3 8.0 + - - +
14L TYR* 1.3 84.5 - - + +
16L LYS* 1.3 61.6 + - - +
18L GLN* 3.3 5.6 + - - +
19L ALA* 3.1 20.1 + - - +
40M VAL* 4.1 21.4 - - + +
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Residues in contact with LYS 16 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2687 T 3.7 33.0 + - - +
2697 A 2.8 31.6 + - - -
728 T 3.3 33.1 + - - +
738 A 3.9 21.7 + - - +
12L GLN 3.1 13.7 + - - +
15L ALA* 1.3 77.4 - - - +
17L TRP* 1.3 66.4 + - - +
19L ALA* 3.1 4.5 + - - +
20L LYS* 3.0 26.2 + - + +
37M VAL* 4.7 8.7 - - + -
40M VAL* 3.9 18.6 - - + -
44M ASN* 5.5 2.2 - - - +
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Residues in contact with TRP 17 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2797 A 3.8 34.5 + - + -
718 A 3.8 27.8 + - + -
728 T 3.8 20.3 - - - +
41K ALA* 4.1 20.2 - - + -
42K GLN* 4.2 7.4 - - + -
45K PHE* 3.5 52.6 - + + -
13L ARG 3.0 19.7 + - - +
14L TYR* 3.0 15.2 + + - +
16L LYS* 1.3 75.5 - - - +
18L GLN* 1.3 93.5 + - - +
20L LYS* 3.4 2.2 + - - +
21L PHE* 2.8 53.0 + + + +
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Residues in contact with GLN 18 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42K GLN* 3.2 40.2 - - - +
14L TYR* 2.7 58.2 + - + +
15L ALA* 3.5 6.7 - - - +
17L TRP* 1.3 82.2 - - - +
19L ALA* 1.3 62.6 + - - +
21L PHE* 3.2 6.3 + - - +
22L ASN* 2.9 63.3 + - - +
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Residues in contact with ALA 19 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15L ALA 3.1 9.4 + - - +
16L LYS* 3.1 10.6 + - - +
18L GLN* 1.3 80.2 - - - +
20L LYS* 1.3 58.4 + - - +
22L ASN* 3.5 10.1 + - - +
23L ALA* 3.0 26.9 + - - +
36M ASN* 3.4 34.4 - - - +
37M VAL* 3.7 17.0 - - + -
40M VAL* 4.5 4.5 - - + -
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Residues in contact with LYS 20 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2697 A 2.8 30.3 + - - +
2707 T 3.1 25.1 + - - -
718 A 3.4 44.9 + - + +
728 T 3.2 21.1 + - - +
16L LYS* 3.0 22.2 + - + +
17L TRP 3.9 2.9 - - - +
19L ALA* 1.3 75.8 - - - +
21L PHE* 1.3 65.9 + - - +
23L ALA* 3.3 3.9 + - + +
24L PHE* 3.0 24.1 + - - +
33M ILE* 3.9 20.0 - - + -
37M VAL* 3.6 17.0 - - + -
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Residues in contact with PHE 21 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2797 A 5.7 2.5 - + - -
2807 T 4.5 23.3 - - + -
708 T 6.0 1.3 - - - -
718 A 5.2 2.8 - - - -
34K LEU* 3.9 30.1 - - + -
37K VAL* 4.5 4.9 - - + -
38K SER* 3.5 37.7 - - - -
41K ALA* 4.5 9.0 - - + -
42K GLN* 5.8 0.2 - - + -
17L TRP* 2.8 51.9 + + + +
18L GLN* 3.6 10.8 - - - +
20L LYS* 1.3 76.4 - - - +
22L ASN* 1.3 71.4 - - - +
24L PHE* 3.3 11.3 + + - +
25L SER* 3.0 24.2 + - - -
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Residues in contact with ASN 22 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38K SER* 5.5 2.3 + - - -
42K GLN* 4.6 3.1 + - - -
18L GLN* 2.9 52.1 + - - +
19L ALA* 3.5 8.3 - - - +
21L PHE* 1.3 79.9 - - - +
23L ALA* 1.3 62.7 + - - +
25L SER* 2.6 25.9 + - - -
26L ASN* 3.6 4.2 + - - +
32M THR* 5.2 0.2 - - - +
36M ASN* 4.0 12.1 - - - +
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Residues in contact with ALA 23 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19L ALA 3.0 15.1 + - - +
20L LYS* 3.5 8.7 - - - +
22L ASN* 1.3 79.0 - - - +
24L PHE* 1.3 63.8 + - - +
26L ASN* 3.1 21.5 + - - +
29L VAL* 3.3 10.9 - - - +
32M THR* 3.6 14.8 - - + -
33M ILE* 3.8 28.3 - - + -
36M ASN* 3.5 16.1 - - - +
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Residues in contact with PHE 24 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2817 A 6.0 0.2 - - - -
708 T 3.7 51.4 - - + +
718 A 5.4 3.1 - - - +
24K PHE* 4.4 9.4 - + - -
34K LEU* 3.5 30.5 - - + -
20L LYS 3.0 17.2 + - - +
21L PHE* 3.7 11.7 - + - +
23L ALA* 1.3 77.6 - - - +
25L SER* 1.3 62.5 + - - +
26L ASN 3.0 1.4 + - - -
29L VAL* 3.8 5.8 - - - -
30L ALA* 3.3 44.6 + - - +
33L ILE* 4.2 19.5 - - + -
34L LEU* 4.0 25.1 - - + -
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Residues in contact with SER 25 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31K SER* 3.4 21.4 - - - +
34K LEU* 3.8 37.2 - - - -
35K SER* 4.5 6.1 - - - -
38K SER* 4.7 7.5 + - - -
21L PHE* 3.0 15.0 + - - -
22L ASN* 2.6 23.6 + - - -
24L PHE* 1.3 75.7 - - - +
26L ASN* 1.3 61.0 + - - +
27L PRO* 3.2 5.0 - - - +
30L ALA* 4.9 0.9 - - - -
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Residues in contact with ASN 26 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22L ASN 3.6 2.7 + - - +
23L ALA 3.1 15.0 + - - +
24L PHE 3.0 1.2 + - - -
25L SER* 1.3 78.8 + - - +
27L PRO* 1.4 67.1 - - - +
28L THR* 2.9 24.4 + - - -
29L VAL* 2.7 37.2 + - + -
30L ALA* 2.8 12.1 + - - -
32M THR* 4.0 19.2 + - + +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il